Multiple sequence alignment - TraesCS2A01G106300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G106300 chr2A 100.000 2661 0 0 1 2661 58507143 58504483 0 4915
1 TraesCS2A01G106300 chr2A 96.761 1914 55 6 1 1909 733073864 733075775 0 3184
2 TraesCS2A01G106300 chr2A 99.468 752 2 2 1910 2661 58498190 58497441 0 1365
3 TraesCS2A01G106300 chr2A 98.283 757 9 4 1907 2661 85673754 85674508 0 1323
4 TraesCS2A01G106300 chr7A 96.970 1914 51 6 1 1909 722692713 722690802 0 3206
5 TraesCS2A01G106300 chr6A 96.862 1912 52 7 1 1909 554918368 554920274 0 3192
6 TraesCS2A01G106300 chr6A 98.406 753 9 3 1910 2661 584791405 584792155 0 1321
7 TraesCS2A01G106300 chr5A 96.815 1915 54 6 1 1909 624937748 624935835 0 3192
8 TraesCS2A01G106300 chr4A 96.813 1914 55 5 1 1909 592482780 592484692 0 3192
9 TraesCS2A01G106300 chr4A 96.813 1914 55 5 1 1909 592761586 592763498 0 3192
10 TraesCS2A01G106300 chr4A 96.708 1914 57 5 1 1909 593049664 593051576 0 3181
11 TraesCS2A01G106300 chr4A 98.541 754 7 4 1907 2658 349724217 349724968 0 1328
12 TraesCS2A01G106300 chr1A 96.813 1914 53 7 1 1909 21070270 21068360 0 3190
13 TraesCS2A01G106300 chr3A 96.761 1914 55 6 1 1909 42788380 42786469 0 3184
14 TraesCS2A01G106300 chr7B 98.539 753 8 3 1910 2661 440859315 440860065 0 1327
15 TraesCS2A01G106300 chr6B 98.539 753 8 3 1910 2661 351838087 351837337 0 1327
16 TraesCS2A01G106300 chr6B 98.039 765 10 5 1899 2661 351856282 351855521 0 1325
17 TraesCS2A01G106300 chr6B 98.406 753 9 3 1910 2661 522913122 522913872 0 1321
18 TraesCS2A01G106300 chr5B 98.406 753 8 4 1910 2661 696913899 696914648 0 1321


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G106300 chr2A 58504483 58507143 2660 True 4915 4915 100.000 1 2661 1 chr2A.!!$R2 2660
1 TraesCS2A01G106300 chr2A 733073864 733075775 1911 False 3184 3184 96.761 1 1909 1 chr2A.!!$F2 1908
2 TraesCS2A01G106300 chr2A 58497441 58498190 749 True 1365 1365 99.468 1910 2661 1 chr2A.!!$R1 751
3 TraesCS2A01G106300 chr2A 85673754 85674508 754 False 1323 1323 98.283 1907 2661 1 chr2A.!!$F1 754
4 TraesCS2A01G106300 chr7A 722690802 722692713 1911 True 3206 3206 96.970 1 1909 1 chr7A.!!$R1 1908
5 TraesCS2A01G106300 chr6A 554918368 554920274 1906 False 3192 3192 96.862 1 1909 1 chr6A.!!$F1 1908
6 TraesCS2A01G106300 chr6A 584791405 584792155 750 False 1321 1321 98.406 1910 2661 1 chr6A.!!$F2 751
7 TraesCS2A01G106300 chr5A 624935835 624937748 1913 True 3192 3192 96.815 1 1909 1 chr5A.!!$R1 1908
8 TraesCS2A01G106300 chr4A 592482780 592484692 1912 False 3192 3192 96.813 1 1909 1 chr4A.!!$F2 1908
9 TraesCS2A01G106300 chr4A 592761586 592763498 1912 False 3192 3192 96.813 1 1909 1 chr4A.!!$F3 1908
10 TraesCS2A01G106300 chr4A 593049664 593051576 1912 False 3181 3181 96.708 1 1909 1 chr4A.!!$F4 1908
11 TraesCS2A01G106300 chr4A 349724217 349724968 751 False 1328 1328 98.541 1907 2658 1 chr4A.!!$F1 751
12 TraesCS2A01G106300 chr1A 21068360 21070270 1910 True 3190 3190 96.813 1 1909 1 chr1A.!!$R1 1908
13 TraesCS2A01G106300 chr3A 42786469 42788380 1911 True 3184 3184 96.761 1 1909 1 chr3A.!!$R1 1908
14 TraesCS2A01G106300 chr7B 440859315 440860065 750 False 1327 1327 98.539 1910 2661 1 chr7B.!!$F1 751
15 TraesCS2A01G106300 chr6B 351837337 351838087 750 True 1327 1327 98.539 1910 2661 1 chr6B.!!$R1 751
16 TraesCS2A01G106300 chr6B 351855521 351856282 761 True 1325 1325 98.039 1899 2661 1 chr6B.!!$R2 762
17 TraesCS2A01G106300 chr6B 522913122 522913872 750 False 1321 1321 98.406 1910 2661 1 chr6B.!!$F1 751
18 TraesCS2A01G106300 chr5B 696913899 696914648 749 False 1321 1321 98.406 1910 2661 1 chr5B.!!$F1 751


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
83 84 0.036732 CTACTTGGTGCAGGCAAGGA 59.963 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2087 0.652592 CGCTGGTCATCGGTGATTTC 59.347 55.0 0.0 0.0 36.6 2.17 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.486982 GTGCTGATGTGTTTGAGCTCAT 59.513 45.455 19.04 0.00 32.41 2.90
83 84 0.036732 CTACTTGGTGCAGGCAAGGA 59.963 55.000 0.00 0.00 0.00 3.36
130 131 4.666512 AGTGCTGTAAAATGGACAAGGAT 58.333 39.130 0.00 0.00 0.00 3.24
132 133 4.458989 GTGCTGTAAAATGGACAAGGATGA 59.541 41.667 0.00 0.00 0.00 2.92
194 197 2.004017 GCGTTGATGTCATACCGGAAA 58.996 47.619 9.46 0.00 0.00 3.13
209 212 2.235402 CCGGAAAGGTACCTGCTAAGAA 59.765 50.000 17.14 0.00 34.51 2.52
405 408 2.087009 GTGCAGCACGTACCGAGAC 61.087 63.158 10.47 0.00 0.00 3.36
457 460 4.680237 CCGACTGCTGCAACGGGA 62.680 66.667 28.10 0.00 41.41 5.14
607 610 0.544223 TGTGCCCAGTTACACACACT 59.456 50.000 0.00 0.00 41.67 3.55
610 613 3.181449 TGTGCCCAGTTACACACACTATT 60.181 43.478 0.00 0.00 41.67 1.73
690 693 9.261180 GCATCAAGATAACACAGCTAACTTATA 57.739 33.333 0.00 0.00 0.00 0.98
880 883 6.352222 CCATCAAACTAGGTCTGTAACTCCAT 60.352 42.308 0.00 0.00 0.00 3.41
913 916 4.798433 TGCTCAGTTGCACCGAAT 57.202 50.000 0.00 0.00 38.12 3.34
956 961 4.667668 GCTGTGTTAGTTCGAGCATCAAAG 60.668 45.833 1.01 3.51 33.17 2.77
1266 1272 5.999205 TGTTTTTCATGTTCTGCCCATAT 57.001 34.783 0.00 0.00 0.00 1.78
1376 1382 4.099266 ACAAAATGTACTGTGTGGTTGCAT 59.901 37.500 0.00 0.00 0.00 3.96
1481 1488 3.197790 CGTTGGAGGCTGCATCCG 61.198 66.667 26.05 11.71 39.91 4.18
1752 1763 3.866651 AGTGGACACATTCAGCATCTAC 58.133 45.455 5.14 0.00 0.00 2.59
1760 1771 5.069119 ACACATTCAGCATCTACGATTCCTA 59.931 40.000 0.00 0.00 0.00 2.94
2157 2172 2.757868 CCACGTCTCCTCTTCTTGATCT 59.242 50.000 0.00 0.00 0.00 2.75
2318 2333 2.199652 CCAAAGGCCAAGGCGTTCA 61.200 57.895 18.14 0.00 46.55 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.304123 CGCAACAAATTTCTGGTTCGGTA 60.304 43.478 0.00 0.00 0.00 4.02
194 197 2.188817 CCACCTTCTTAGCAGGTACCT 58.811 52.381 9.21 9.21 43.30 3.08
405 408 1.966451 GACTTGTTCAGGTGGCCGG 60.966 63.158 0.00 0.00 0.00 6.13
607 610 4.041075 TGTTCTGTCCAAGTGGCTACAATA 59.959 41.667 2.02 0.00 34.44 1.90
610 613 1.765904 TGTTCTGTCCAAGTGGCTACA 59.234 47.619 2.02 0.00 34.44 2.74
913 916 0.458669 GTGCGCAACTAGGTAGCCTA 59.541 55.000 14.00 0.00 34.61 3.93
1266 1272 2.563620 TGGTACTTGGATTGTAGTCGCA 59.436 45.455 0.00 0.00 0.00 5.10
1343 1349 6.127869 ACACAGTACATTTTGTGCAACTAACA 60.128 34.615 11.68 0.00 46.59 2.41
1376 1382 2.426522 GCAACCAGCACTGATGTTCTA 58.573 47.619 0.00 0.00 44.79 2.10
1423 1429 8.082242 TCACGATCACCTGTGTAATAATCATAG 58.918 37.037 0.00 0.00 37.38 2.23
1481 1488 3.844577 ATCATCAGAAGCTTGTGCAAC 57.155 42.857 18.38 0.00 42.74 4.17
1873 1887 8.100791 ACTTTTGTTGATACATTAGGAGCACTA 58.899 33.333 0.00 0.00 33.44 2.74
2073 2087 0.652592 CGCTGGTCATCGGTGATTTC 59.347 55.000 0.00 0.00 36.60 2.17
2157 2172 0.263172 CTCTCCTCCCTCCCTTGCTA 59.737 60.000 0.00 0.00 0.00 3.49
2318 2333 3.631346 GGAGAGGAGGGACTTCATACCTT 60.631 52.174 0.00 0.00 41.55 3.50



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.